In a simple mass spectrometry (MS) system, ions of a sample are formed in an ion source, such as for instance an Electron Impact (EI) source or an Atmospheric Pressure Ionization (API) source. The ions then pass through a mass analyzer, such as for instance a quadrupole (Q) or a time of flight (TOF) device, for detection. The detected ions include at least one of molecular ions, fragments of the molecular ions, and fragments of other fragment ions.
Tandem mass spectrometry (MS/MS) systems have also been developed, which are characterized by having two or more sequential stages of mass analysis and an intermediate ion fragmentation region, where ions from the first stage are fragmented into product ions for analysis within the second stage. There are two basic types of tandem mass spectrometers, namely those that are “tandem in space” and those that are “tandem in time.” Tandem in space mass spectrometers, such as for instance triple quadrupole (QqQ) and quadrupole-time of flight (Q-TOF) devices, have two distinct mass analyzers, one for precursor ion selection and one for product ion detection and/or measurement. An ion fragmentation device, such as for instance a gas-filled collision cell, is disposed between the two mass analyzers for receiving ions from the first mass analyzer and for fragmenting the ions to form product ions for introduction into the second mass analyzer. Tandem in time instruments, on the other hand, have one mass analyzer that analyses both the precursor ions and the product ions, but that does so sequentially in time. Ion trap and FT-ICR are two common types of mass spectrometer that are used for tandem in time MS/MS.
Several MS/MS scan types, in particular “product ion scan”, “precursor ion scan” and “neutral loss scan,” are known. Performing a “product ion scan” is done by selecting a particular precursor ion in the first MS stage, and then obtaining in the second MS stage a full scan of the product ions that are formed when the selected precursor ion is fragmented. This method is useful for determining structural information relating to a precursor ion of known molecular weight. For instance, two distinct precursor ions of similar molecular weight but different structure can be differentiated based on the product ions they typically fragment into. A “product ion scan” is often used in combination with liquid chromatography (LC-MS/MS). The product ion scan is considered to be data dependent when the mass spectral precursor is automatically selected based upon a previous scan acquired without fragmentation. The mass analyzer then makes a full scan of the product ions resulting from fragmentation of the selected precursor ion of interest.
A “precursor scan,” is a method that has a fixed product ion selection for the second MS stage, while using the first MS stage to scan all of the pre-fragmentation precursor ions in a sample. Detection is limited to only those molecules/compounds in the sample that produce a specific product ion when fragmented.
Finally, “neutral loss scan” is a method that supports detection of all precursor ions that lose a particular mass during fragmentation. The second stage mass analyzer scans the ions together with the first stage mass analyzer, but with a predetermined offset corresponding to the lost mass. Neutral loss scans are used for screening experiments, where a group of compounds all give the same mass loss during fragmentation.
Each of the above-mentioned tandem scan types represents a compromise approach, in which the amount of information that is obtained from a sample is balanced against the various limitations of the mass analysis and/or separation systems. In particular, each scan type provides only partial two-dimensional mass spectral (2DMS) data. True 2DMS (also referred to as “all mass MS/MS”) requires a data independent approach, in which substantially all of the ions (or all of the ions within a particular mass range of interest) that are produced from a sample are subjected to fragmentation and product ion scanning. Accordingly, a complete two-dimensional MS/MS map comprises product ion mass spectral information for every precursor ion in a sample. The different MS/MS scans such as “product ion scan”, “precursor ion scan” and “neutral loss scan” are all subsets of this complete two-dimensional MS/MS map.
Rapidly emerging fields such as proteomics and metabolomics are straining the capabilities of modem, data dependent MS/MS systems. Analysis of complex mixtures is typical, which often involves a liquid chromatography pre-separation step that is followed by one or more MS/MS scan events. Unfortunately, in a LC-MS/MS system the precursor ions duration time is limited because additional peaks elute from the LC device in a specified time period. Normally, there is not enough time to do different types of scans in a single LC run. It is also not unusual that several precursor ions co-elute at the same time. Simply put, in many cases, there is insufficient time to fully analyze all precursor ions using data dependent scan methods. For this reason, acquisition of true two-dimensional data is desirable, which would then allow simple data mining for the extraction of “precursor,” “product,” and “neutral loss” information.
One approach is to use an ion trap as the first mass analyzer for storing precursor ions and/or accumulating precursor ions over time. By scanning the precursor ions out of the ion trap in a mass selective fashion, it is possible to obtain product ion scans for each precursor ion using a second, rapid scanning mass analyzer such as for instance a TOF. A problem is that there is a conflict between speed of analysis (i.e. number of MS/MS experiments per second) and space charge effects. To ensure that the TOF mass analyzer detects a sufficient number of fragmented ions to give sound experimental data, ever-increasing ion abundances must be stored upstream, particularly where more than one precursor ion is to be fragmented and analyzed. The need for high ion abundances upstream in the first analyzer is in conflict with the fact that the greater the ion abundance, the worse the resolution and accuracy of this analyzer becomes due to space charge effects. For emerging high-throughput applications such as proteomics and metabolomics, it is important to provide heretofore-unattainable speeds of analysis, on the order of hundreds of MS/MS spectra per second. This in turn requires both efficient, space-charge tolerant utilization of the incoming ions and fast, on the order of milliseconds, analysis of the products of each individual precursor m/z.
In U.S. Pat. No. 6,770,871, issued Aug. 3, 2004 to Wang et al., there is described a tandem mass spectrometer including two mass analyzers, with an ion fragmentation device interposed between the two mass analyzers. The first mass analyzer is a non-destructive mass analyzer, such as an ion trap, to initially collect and hold precursor ions and sequentially release precursor ions of known mass to charge ratio. The released precursor ions pass through the fragmentation device, such as a collision cell, where the precursor ions are fragmented into product ions. These product ions then pass on to the second mass analyzer. The second mass analyzer is of a high-speed, full spectrum type, such as a time of flight analyzer, so that a full spectrum of mass data is provided for the product ions, to go with precursor ion mass spectrum data from the first mass analyzer. The primary disadvantage of this design is that the three-dimensional ion trap has insufficient ion storage capacity to produce high quality MS/MS spectra for more than a couple of components at one time. This disadvantage severely restricts the potential performance when operating in true 2DMS mode. Wang et al. suggest the use of a linear ion trap, but positively state a preference for the three dimensional type.
In PCT Publication No. WO 2004/083805, Makarov et al. describe a tandem mass spectrometer including a linear ion trap and an orthogonal acceleration time of flight analyzer (oa-TOF), with a specially designed planar collision cell disposed between the two mass analyzers. In particular, the linear ion trap is operated in radial ejection mode, such that precursor ions stored within the trap are scanned out through a slit-shaped opening in one of the electrodes or between electrodes, to produce a ribbon shaped beam of ions for injection into the collision cell. Advantageously, the linear ion trap is capable of storing a greater number of ions compared to the three-dimensional ion trap. However, because the ion beam is spread out laterally, it cannot be directly injected into a conventional TOF analyzer. Accordingly, the collision cell has been adapted to a planar form to capture the ribbon shaped ion beam from the linear trap, dissociate the ions, and then laterally focus the beam to a narrow circular cross section for optimal injection into the oa-TOF. This is a highly complex and non-standard collision cell design, both from a mechanical and from an electrical design point of view. Furthermore, the inlet end of the planar collision cell has a large cross-sectional area to accept the ribbon shaped ion beam, which would produce a large load on the pumping system from the collision gas that would leak from this orifice. This load could be sufficiently large to require differential pumping around the collision cell, adding to the overall complexity of the system.
There remains a need in the mass spectrometry art for a system and method that supports data independent tandem MS/MS of complex samples while avoiding the problems and complexities of the approaches outlined above.